1
|
Kong Y, Riebe J, Feßner M, Schaller T, Wölper C, Stappert F, Meckelmann SW, Krajnc M, Weyrauch P, Schmitz OJ, Merten C, Niemeyer J, Hu X, Meckenstock RU. A CoA-Transferase and Acyl-CoA Dehydrogenase Convert 2-(Carboxymethyl)cyclohexane-1-Carboxyl-CoA During Anaerobic Naphthalene Degradation. Environ Microbiol 2024; 26:e70013. [PMID: 39702997 DOI: 10.1111/1462-2920.70013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 11/17/2024] [Accepted: 11/27/2024] [Indexed: 12/21/2024]
Abstract
The CoA thioester of 2-(carboxymethyl)cyclohexane-1-carboxylic acid has been identified as a metabolite in anaerobic naphthalene degradation by the sulfate-reducing culture N47. This study identified and characterised two acyl-CoA dehydrogenases (ThnO/ThnT) and an intramolecular CoA-transferase (ThnP) encoded within the substrate-induced thn operon, which contains genes for anaerobic degradation of naphthalene. ThnP is a CoA transferase belonging to the family I (Cat 1 subgroup) that catalyses the intramolecular CoA transfer from the carboxyl group of 2-(carboxymethyl)cyclohexane-1-carboxyl-CoA to its carboxymethyl moiety, forming 2-carboxycyclohexylacetyl-CoA. Neither acetyl-CoA nor succinyl-CoA functions as an exogenous CoA donor for this reaction. The flavin-dependent homotetrameric dehydrogenase ThnO is specific for (1R,2R)-2-carboxycyclohexylacetyl-CoA with an apparent Km value of 61.5 μM, whereas ThnT is a promiscuous enzyme catalysing the same reaction at lower rates. Identifying these three enzymes confirmed the involvement of the thn gene cluster in the anaerobic naphthalene degradation pathway. This study establishes a modified metabolic pathway for anaerobic naphthalene degradation upstream of 2-(carboxymethyl)cyclohexane-1-carboxyl-CoA and provides further insight into the subsequent second-ring cleavage reaction.
Collapse
Affiliation(s)
- Yachao Kong
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- Institute for Environmental Microbiology and Biotechnology, Aquatic Microbiology, University of Duisburg-Essen, Essen, Germany
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jan Riebe
- Organic Chemistry, Faculty of Chemistry and Center for Nanointegration, Duisburg-Essen (CENIDE), University of Duisburg-Essen, Essen, Germany
| | - Malte Feßner
- Organic Chemistry II, Faculty of Chemistry and Biochemistry, Ruhr Universität Bochum, Bochum, Germany
| | - Torsten Schaller
- Organic Chemistry, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christoph Wölper
- Inorganic Chemistry, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Florian Stappert
- Applied Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Sven W Meckelmann
- Applied Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Matthias Krajnc
- Organic Chemistry, Faculty of Chemistry and Center for Nanointegration, Duisburg-Essen (CENIDE), University of Duisburg-Essen, Essen, Germany
| | - Philip Weyrauch
- Institute for Environmental Microbiology and Biotechnology, Aquatic Microbiology, University of Duisburg-Essen, Essen, Germany
| | - Oliver J Schmitz
- Applied Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christian Merten
- Organic Chemistry II, Faculty of Chemistry and Biochemistry, Ruhr Universität Bochum, Bochum, Germany
| | - Jochen Niemeyer
- Organic Chemistry, Faculty of Chemistry and Center for Nanointegration, Duisburg-Essen (CENIDE), University of Duisburg-Essen, Essen, Germany
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- Qingdao Marine Science and Technology Center, Laboratory for Marine Biology and Biotechnology, Qingdao, China
| | - Rainer U Meckenstock
- Institute for Environmental Microbiology and Biotechnology, Aquatic Microbiology, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
2
|
Kaplieva-Dudek I, Samak NA, Bormann J, Kaschani F, Kaiser M, Meckenstock RU. Characterization of 2-phenanthroate:CoA ligase from the sulfate-reducing, phenanthrene-degrading enrichment culture TRIP. Appl Environ Microbiol 2024; 90:e0129624. [PMID: 39248461 PMCID: PMC11497795 DOI: 10.1128/aem.01296-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 08/01/2024] [Indexed: 09/10/2024] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are chemically stable pollutants that are poorly degraded by microorganisms in anoxic sediments. The anaerobic degradation pathway of PAHs such as phenanthrene starts with a carboxylation reaction forming phenanthroic acid. In this study, we identified and characterized the next enzyme in the pathway, the 2-phenanthroate:CoA ligase involved in the ATP-dependent formation of 2-phenanthroyl-CoA from cell-free extracts of the sulfate-reducing enrichment culture TRIP grown anaerobically with phenanthrene. The identified gene sequence indicated that 2-phenanthroate:CoA ligase belongs to the phenylacetate:CoA ligase-like enzyme family. Based on the sequence, we predict a two-domain structure of the 2-phenanthroate:CoA ligase with a typical large N-terminal and a smaller C-terminal domain. Partial purification of 2-phenanthroate:CoA ligase allowed us to identify the coding gene in the genome. 2-Phenanthroate:CoA ligase gene was heterologously expressed in Escherichia coli. Characterization of the 2-phenanthroate:CoA ligase was performed using the partially purified enzyme from cell-free extract and the purified recombinant enzyme. Testing all possible phenanthroic acid isomers as substrate for the ligase reaction showed that 2-phenanthroic acid is the preferred substrate and only 3-phenanthroic acid can be utilized to a minor extent. This also suggests that the product of the prior carboxylase reaction is 2-phenanthroic acid. 2-Phenanthroate:CoA ligase has an optimal activity at pH 7.5 and is oxygen-insensitive, analogous to other aryl-CoA ligases. In contrast to aryl-Coenzyme A ligases reported in the literature, which need Mg2+ as cofactor, 2-phenanthroate:CoA ligase showed greatest activity with a combination of 5 mM MgCl2 and 5 mM KCl. Furthermore, a substrate inhibition was observed at ATP concentrations above 1 mM and the enzyme was also active with ADP. IMPORTANCE Polycyclic aromatic hydrocarbons (PAHs) constitute a class of very toxic and persistent pollutants in the environment. However, the anaerobic degradation of three-ring PAHs such as phenanthrene is barely investigated. The initial degradation step starts with a carboxylation followed by a CoA‑thioesterification reaction performed by an aryl-CoA ligase. The formation of a CoA-thioester is an important step in the degradation pathway of aromatic compounds because the CoA-ester is needed for all downstream biochemical reactions in the pathway. Furthermore, we provide biochemical proof for the identification of the first genes for anaerobic phenanthrene degradation. Results presented here provide information about the biochemical and structural properties of the purified 2‑phenanthroate:CoA ligase and expand our knowledge of aryl-CoA ligases.
Collapse
Affiliation(s)
- I. Kaplieva-Dudek
- Environmental Microbiology and Biotechnology (EMB), Aquatic Microbiology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Nadia A. Samak
- Environmental Microbiology and Biotechnology (EMB), Aquatic Microbiology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Jenny Bormann
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- Analytics Core Facility Essen, ZMB, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Farnusch Kaschani
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- Analytics Core Facility Essen, ZMB, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Markus Kaiser
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Rainer U. Meckenstock
- Environmental Microbiology and Biotechnology (EMB), Aquatic Microbiology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
3
|
Obayori OS, Salam LB, Ashade AO, Oseni TD, Kalu MD, Mustapha FM. An animal charcoal contaminated cottage industry soil highlighted by halophilic archaea dominance and decimation of bacteria. World J Microbiol Biotechnol 2024; 40:327. [PMID: 39299940 DOI: 10.1007/s11274-024-04136-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 09/09/2024] [Indexed: 09/22/2024]
Abstract
An animal charcoal contaminated cottage industry soil in Lagos, Nigeria (ACGT) was compared in an ex post facto study with a nearby unimpacted soil (ACGC). Hydrocarbon content was higher than regulatory limits in ACGT (180.2 mg/kg) but lower in ACGC (19.28 mg/kg). Heavy metals like nickel, cadmium, chromium and lead were below detection limit in ACGC. However, all these metals, except cadmium, were detected in ACGT, but at concentrations below regulatory limits. Furthermore, copper (253.205 mg/kg) and zinc (422.630 mg/kg) were above regulatory limits in ACGT. Next generation sequencing revealed that the procaryotic community was dominated by bacteria in ACGC (62%) while in ACGT archaea dominated (76%). Dominant phyla in ACGC were Euryarchaeota (37%), Pseudomonadota (16%) and Actinomycetota (12%). In ACGT it was Euryarchaeota (76%), Bacillota (9%), Pseudomonadota (7%) and Candidatus Nanohaloarchaeota (5%). Dominant Halobacteria genera in ACGT were Halobacterium (16%), Halorientalis (16%), unranked halophilic archaeon (13%) Salarchaeum (6%) and Candidatus Nanohalobium (5%), whereas ACGC showed greater diversity dominated by bacterial genera Salimicrobium (7%) and Halomonas (3%). Heavy metals homeostasis genes, especially for copper, were fairly represented in both soils but with bacterial taxonomic affiliations. Sites like ACGT, hitherto poorly studied and understood, could be sources of novel bioresources.
Collapse
Affiliation(s)
| | - Lateef Babatunde Salam
- Microbiology Unit, Department of Biological Sciences, Elizade University, Ilara-Mokin, Ondo State, Nigeria
| | - Ahmeed Olalekan Ashade
- Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria
| | | | - Mandy Divine Kalu
- Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria
| | | |
Collapse
|
4
|
Mohamad Shahimin MF, Siddique T. Uncovering Anaerobic Hydrocarbon Biodegradation Pathways in Oil Sands Tailings from Two Different Tailings Ponds via Metabolite and Functional Gene Analyses. Appl Biochem Biotechnol 2024; 196:6363-6377. [PMID: 38376742 DOI: 10.1007/s12010-024-04855-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2024] [Indexed: 02/21/2024]
Abstract
Oil sands tailings, a slurry of alkaline water, silt, clay, unrecovered bitumen, and residual hydrocarbons generated during bitumen extraction, are contained in ponds. Indigenous microbes metabolize hydrocarbons and emit greenhouse gases from the tailings. Metabolism of hydrocarbons in tailings ponds of two operators, namely, Canadian Natural Upgrading Limited (CNUL) and Canadian Natural Resources Limited (CNRL), has not been comprehensively investigated. Previous reports have revealed sequential and preferential hydrocarbon degradation of alkanes in primary cultures established from CNUL and CNRL tailings amended separately with mixtures of hydrocarbons (n-alkanes, iso-alkanes, paraffinic solvent, or naphtha). In this study, activation pathway of hydrocarbon biodegradation in these primary cultures was investigated. The functional gene analysis revealed that fumarate addition was potentially the primary activation pathway of alkanes in all cultures. However, the metabolite analysis only detected transient succinylated 2-methylpentane and 2-methylbutane metabolites during initial methanogenic biodegradation of iso-alkanes and paraffinic solvent in all CNUL and CNRL cultures amended with iso-alkanes and paraffinic solvent. Under sulfidogenic conditions (prepared only with CNUL tailings amended with iso-alkanes), succinylated 2-methylpentane persisted throughout incubation period of ~ 1100 days, implying dead-end nature of the metabolite. Though no metabolite was detected in n-alkanes- and naphtha-amended cultures during incubation, assA/masD genes related to Peptococcaceae were amplified in all CNUL and CNRL primary cultures. The findings of this present study suggest that microbial communities in different tailings ponds can biodegrade hydrocarbons through fumarate addition as activation pathway under methanogenic and sulfidogenic conditions.
Collapse
Affiliation(s)
- Mohd Faidz Mohamad Shahimin
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2G7, Canada.
- Faculty of Chemical Engineering & Technology, Universiti Malaysia Perlis, Aras 2, Blok S2, UniCITI Alam Campus, 02100, Padang Besar, Perlis, Malaysia.
| | - Tariq Siddique
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2G7, Canada
| |
Collapse
|
5
|
Laczi K, Bodor A, Kovács T, Magyar B, Perei K, Rákhely G. Methanogenesis coupled hydrocarbon biodegradation enhanced by ferric and sulphate ions. Appl Microbiol Biotechnol 2024; 108:449. [PMID: 39207532 PMCID: PMC11362221 DOI: 10.1007/s00253-024-13278-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/05/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
Bioremediation provides an environmentally sound solution for hydrocarbon removal. Although bioremediation under anoxic conditions is slow, it can be coupled with methanogenesis and is suitable for energy recovery. By altering conditions and supplementing alternative terminal electron acceptors to the system to induce syntrophic partners of the methanogens, this process can be enhanced. In this study, we investigated a hydrocarbon-degrading microbial community derived from chronically contaminated soil. Various hydrocarbon mixtures were used during our experiments in the presence of different electron acceptors. In addition, we performed whole metagenome sequencing to identify the main actors of hydrocarbon biodegradation in the samples. Our results showed that the addition of ferric ions or sulphate increased the methane yield. Furthermore, the addition of CO2, ferric ion or sulphate enhanced the biodegradation of alkanes. A significant increase in biodegradation was observed in the presence of ferric ions or sulphate in the case of all aromatic components, while naphthalene and phenanthrene degradation was also enhanced by CO2. Metagenome analysis revealed that Cellulomonas sp. is the most abundant in the presence of alkanes, while Ruminococcus and Faecalibacterium spp. are prevalent in aromatics-supplemented samples. From the recovery of 25 genomes, it was concluded that the main pathway of hydrocarbon activation was fumarate addition in both Cellulomonas, Ruminococcus and Faecalibacterium. Chloroflexota bacteria can utilise the central metabolites of aromatics biodegradation via ATP-independent benzoyl-CoA reduction. KEY POINTS: • Methanogenesis and hydrocarbon biodegradation were enhanced by Fe3+ or SO42- • Cellulomonas, Ruminococcus and Faecalibacterium can be candidates for the main hydrocarbon degraders • Chloroflexota bacteria can utilise the central metabolites of aromatics degradation.
Collapse
Affiliation(s)
- Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary.
- Biological Research Centre, Institute of Plant Biology, Hungarian Research Network, Szeged, Hungary.
| | - Attila Bodor
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Biological Research Centre, Institute of Biophysics, Hungarian Research Network, Szeged, Hungary
| | - Tamás Kovács
- Department of Biotechnology, Nanophage Therapy Center, Enviroinvest Corporation, Pécs, Hungary
| | | | - Katalin Perei
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Biological Research Centre, Institute of Biophysics, Hungarian Research Network, Szeged, Hungary
| |
Collapse
|
6
|
Zhou N, Guo H, Zhang Z, Wang H. The discrepant metabolic pathways of PAHs by facultative anaerobic bacteria under aerobic and nitrate-reducing conditions. CHEMOSPHERE 2024; 351:141230. [PMID: 38237784 DOI: 10.1016/j.chemosphere.2024.141230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/07/2024] [Accepted: 01/14/2024] [Indexed: 01/28/2024]
Abstract
Studies regarding the facultative anaerobic biodegradation of polycyclic aromatic hydrocarbons (PAHs) were still in the initial stage. In this study, a facultative anaerobe which was identified as Bacillus Firmus and named as PheN7 was firstly isolated from the mixed petroleum-polluted soil samples using phenanthrene and nitrate as the solo carbon resource and electron acceptor under anaerobic condition. The degradation rates of PheN7 towards phenanthrene were detected as 33.17 μM/d, 13.81 μM/d and 7.11 μM/d at the initial phenanthrene concentration of 250.17 μM with oxygen, nitrate and sulfate as the electron acceptor, respectively. The metabolic pathways toward phenanthrene by PheN7 were deduced combining the metagenome analysis of PheN7 and intermediate metabolites of phenanthrene under aerobic and nitrate-reducing conditions. Dioxygenation and carboxylation were inferred as the initial activation reactions of phenanthrene degradation in these two pathways. This study highlighted the significance of facultative anaerobic bacteria in natural PAHs biodegradation, revealing the discrepant metabolic fates of PAHs by one solo bacteria under aerobic and anaerobic environments.
Collapse
Affiliation(s)
- Nan Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Haijiao Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
7
|
Mock J, Schühle K, Linne U, Mock M, Heider J. A Synthetic Pathway for the Production of Benzylsuccinate in Escherichia coli. Molecules 2024; 29:415. [PMID: 38257328 PMCID: PMC10818641 DOI: 10.3390/molecules29020415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
(R)-Benzylsuccinate is generated in anaerobic toluene degradation by the radical addition of toluene to fumarate and further degraded to benzoyl-CoA by a β-oxidation pathway. Using metabolic modules for benzoate transport and activation to benzoyl-CoA and the enzymes of benzylsuccinate β-oxidation, we established an artificial pathway for benzylsuccinate production in Escherichia coli, which is based on its degradation pathway running in reverse. Benzoate is supplied to the medium but needs to be converted to benzoyl-CoA by an uptake transporter and a benzoate-CoA ligase or CoA-transferase. In contrast, the second substrate succinate is endogenously produced from glucose under anaerobic conditions, and the constructed pathway includes a succinyl-CoA:benzylsuccinate CoA-transferase that activates it to the CoA-thioester. We present first evidence for the feasibility of this pathway and explore product yields under different growth conditions. Compared to aerobic cultures, the product yield increased more than 1000-fold in anaerobic glucose-fermenting cultures and showed further improvement under fumarate-respiring conditions. An important bottleneck to overcome appears to be product excretion, based on much higher recorded intracellular concentrations of benzylsuccinate, compared to those excreted. While no export system is known for benzylsuccinate, we observed an increased product yield after adding an unspecific mechanosensitive channel to the constructed pathway.
Collapse
Affiliation(s)
- Johanna Mock
- Fachbereich Biologe, Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
- Synmikro Center Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
| | - Karola Schühle
- Fachbereich Biologe, Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
| | - Uwe Linne
- Synmikro Center Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
- Fachbereich Chemie, Philipps-University Marburg, Hans-Meerwein-Str. 10, 35043 Marburg, Germany
| | - Marco Mock
- Fachbereich Biologe, Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
| | - Johann Heider
- Fachbereich Biologe, Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
- Synmikro Center Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
| |
Collapse
|
8
|
Johnson LA, Dufour SC, Smith DDN, Manning AJ, Ahmed B, Binette S, Hamoutene D. Descriptive analyses of bacterial communities in marine sediment microcosms spiked with fish wastes, emamectin benzoate, and oxytetracycline. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 268:115683. [PMID: 37976931 DOI: 10.1016/j.ecoenv.2023.115683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/24/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
In marine sediments surrounding salmon aquaculture sites, organic matter (OM) enrichment has been shown to influence resident bacterial community composition; however, additional effects on these communities due to combined use of the sea-lice therapeutant emamectin benzoate (EMB) and the widely used antibiotic oxytetracycline (OTC) are unknown. Here, we use sediment microcosms to assess the influence of OM, EMB, and OTC on benthic bacterial communities. Microcosms consisted of mud or sand sediments enriched with OM (fish and feed wastes) and spiked with EMB and OTC at environmentally-relevant concentrations. Samples were collected from initial matrices at the initiation of the trial and after 110 days for 16 S rRNA gene sequencing of the V3-V4 region and microbiome profiling. The addition of OM in both mud and sand sediments reduced alpha diversities; for example, an average of 1106 amplicon sequence variants (ASVs) were detected in mud with no OM addition, while only 729 and 596 ASVs were detected in mud with low OM and high OM, respectively. Sediments enriched with OM had higher relative abundances of Spirochaetota, Firmicutes, and Bacteroidota. For instance, Spirochaetota were detected in sediments with no OM with a relative abundance range of 0.01-1.2%, while in sediments enriched with OM relative abundance varied from 0.16% to 26.1%. In contrast, the addition of EMB (60 ng/g) or OTC (150 ng/g) did not result in distinct taxonomic shifts in the bacterial communities compared to un-spiked sediments during the timeline of this experiment. EMB and OTC concentrations may have been below effective inhibitor concentrations for taxa in these communities; further work should explore gene content and the presence of antibiotic resistance genes (ARGs) in sediment-dwelling bacteria.
Collapse
Affiliation(s)
- Lisa A Johnson
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB E5B 0E4, Canada
| | - Suzanne C Dufour
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada
| | - Derek D N Smith
- Environment and Climate Change Canada, 335 River Road, Ottawa, ON K1V 1C7, Canada
| | - Anthony J Manning
- Research & Productivity Council (RPC), Fredericton, NB E3B 6Z9, Canada
| | - Bulbul Ahmed
- Research & Productivity Council (RPC), Fredericton, NB E3B 6Z9, Canada
| | - Sherry Binette
- Research & Productivity Council (RPC), Fredericton, NB E3B 6Z9, Canada
| | - Dounia Hamoutene
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB E5B 0E4, Canada.
| |
Collapse
|
9
|
Matturro B, Di Franca ML, Tonanzi B, Cruz Viggi C, Aulenta F, Di Leo M, Giandomenico S, Rossetti S. Enrichment of Aerobic and Anaerobic Hydrocarbon-Degrading Bacteria from Multicontaminated Marine Sediment in Mar Piccolo Site (Taranto, Italy). Microorganisms 2023; 11:2782. [PMID: 38004793 PMCID: PMC10673493 DOI: 10.3390/microorganisms11112782] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Marine sediments act as a sink for the accumulation of various organic contaminants such as polychlorobiphenyls (PCBs). These contaminants affect the composition and activity of microbial communities, particularly favoring those capable of thriving from their biodegradation and biotransformation under favorable conditions. Hence, contaminated environments represent a valuable biological resource for the exploration and cultivation of microorganisms with bioremediation potential. In this study, we successfully cultivated microbial consortia with the capacity for PCB removal under both aerobic and anaerobic conditions. The source of these consortia was a multicontaminated marine sediment collected from the Mar Piccolo (Taranto, Italy), one of Europe's most heavily polluted sites. High-throughput sequencing was employed to investigate the dynamics of the bacterial community of the marine sediment sample, revealing distinct and divergent selection patterns depending on the imposed reductive or oxidative conditions. The aerobic incubation resulted in the rapid selection of bacteria specialized in oxidative pathways for hydrocarbon transformation, leading to the isolation of Marinobacter salinus and Rhodococcus cerastii species, also known for their involvement in aerobic polycyclic aromatic hydrocarbons (PAHs) transformation. On the other hand, anaerobic incubation facilitated the selection of dechlorinating species, including Dehalococcoides mccartyi, involved in PCB reduction. This study significantly contributes to our understanding of the diversity, dynamics, and adaptation of the bacterial community in the hydrocarbon-contaminated marine sediment from one sampling point of the Mar Piccolo basin, particularly in response to stressful conditions. Furthermore, the establishment of consortia with biodegradation and biotransformation capabilities represents a substantial advancement in addressing the challenge of restoring polluted sites, including marine sediments, thus contributing to expanding the toolkit for effective bioremediation strategies.
Collapse
Affiliation(s)
- Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Maria Letizia Di Franca
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Barbara Tonanzi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Magda Di Leo
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Santina Giandomenico
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| |
Collapse
|
10
|
Zehnle H, Otersen C, Benito Merino D, Wegener G. Potential for the anaerobic oxidation of benzene and naphthalene in thermophilic microorganisms from the Guaymas Basin. Front Microbiol 2023; 14:1279865. [PMID: 37840718 PMCID: PMC10570749 DOI: 10.3389/fmicb.2023.1279865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
Unsubstituted aromatic hydrocarbons (UAHs) are recalcitrant molecules abundant in crude oil, which is accumulated in subsurface reservoirs and occasionally enters the marine environment through natural seepage or human-caused spillage. The challenging anaerobic degradation of UAHs by microorganisms, in particular under thermophilic conditions, is poorly understood. Here, we established benzene- and naphthalene-degrading cultures under sulfate-reducing conditions at 50°C and 70°C from Guaymas Basin sediments. We investigated the microorganisms in the enrichment cultures and their potential for UAH oxidation through short-read metagenome sequencing and analysis. Dependent on the combination of UAH and temperature, different microorganisms became enriched. A Thermoplasmatota archaeon was abundant in the benzene-degrading culture at 50°C, but catabolic pathways remained elusive, because the archaeon lacked most known genes for benzene degradation. Two novel species of Desulfatiglandales bacteria were strongly enriched in the benzene-degrading culture at 70°C and in the naphthalene-degrading culture at 50°C. Both bacteria encode almost complete pathways for UAH degradation and for downstream degradation. They likely activate benzene via methylation, and naphthalene via direct carboxylation, respectively. The two species constitute the first thermophilic UAH degraders of the Desulfatiglandales. In the naphthalene-degrading culture incubated at 70°C, a Dehalococcoidia bacterium became enriched, which encoded a partial pathway for UAH degradation. Comparison of enriched bacteria with related genomes from environmental samples indicated that pathways for benzene degradation are widely distributed, while thermophily and capacity for naphthalene activation are rare. Our study highlights the capacities of uncultured thermophilic microbes for UAH degradation in petroleum reservoirs and in contaminated environments.
Collapse
Affiliation(s)
- Hanna Zehnle
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Carolin Otersen
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - David Benito Merino
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| |
Collapse
|
11
|
Bianco F, Race M, Papirio S, Esposito G. Phenanthrene removal from a spent sediment washing solution in a continuous-flow stirred-tank reactor. ENVIRONMENTAL RESEARCH 2023; 228:115889. [PMID: 37054831 DOI: 10.1016/j.envres.2023.115889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023]
Abstract
The issue of polycyclic aromatic hydrocarbons (PAHs) is widespread in marine sediments involving ecological systems and human health. Sediment washing (SW) has proven to be the most effective remediation approach for sediments polluted by PAHs, such as phenanthrene (PHE). However, SW still raises waste handling concerns due to a considerable amount of effluents generated downstream. In this context, the biological treatment of a PHE- and ethanol-containing spent SW solution can represent a highly efficient and environmentally-friendly strategy, but its knowledge is still scarce in scientific literature and no studies have so far been conducted in continuous mode. Therefore, a synthetic PHE-polluted SW solution was biologically treated in a 1 L aerated continuous-flow stirred-tank reactor for 129 days by evaluating the effect of different pH values, aeration flowrates and hydraulic retention times as operating parameters over five successive phases. A PHE removal efficiency of up to 75-94% was achieved by an acclimated PHE-degrading consortium mainly composed of Proteobacteria, Bacteroidota and Firmicutes phyla through biodegradation following the adsorption mechanism. PHE biodegradation, mainly occurring via the benzoate route due to the presence of PAH-related-degrading functional genes and a phthalate accumulation up to 46 mg/L, was also accompanied by a reduction of dissolved organic carbon and ammonia nitrogen above 99% in the treated SW solution.
Collapse
Affiliation(s)
- Francesco Bianco
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via Di Biasio 43, 03043, Cassino, Italy.
| | - Marco Race
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via Di Biasio 43, 03043, Cassino, Italy
| | - Stefano Papirio
- Department of Civil, Architectural and Environmental Engineering, University of Napoli Federico II, Via Claudio 21, 80125, Napoli, Italy
| | - Giovanni Esposito
- Department of Civil, Architectural and Environmental Engineering, University of Napoli Federico II, Via Claudio 21, 80125, Napoli, Italy
| |
Collapse
|
12
|
Madison AS, Sorsby SJ, Wang Y, Key TA. Increasing in situ bioremediation effectiveness through field-scale application of molecular biological tools. Front Microbiol 2023; 13:1005871. [PMID: 36845972 PMCID: PMC9950576 DOI: 10.3389/fmicb.2022.1005871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/28/2022] [Indexed: 02/12/2023] Open
Abstract
Leveraging the capabilities of microorganisms to reduce (degrade or transform) concentrations of pollutants in soil and groundwater can be a cost-effective, natural remedial approach to manage contaminated sites. Traditional design and implementation of bioremediation strategies consist of lab-scale biodegradation studies or collection of field-scale geochemical data to infer associated biological processes. While both lab-scale biodegradation studies and field-scale geochemical data are useful for remedial decision-making, additional insights can be gained through the application of Molecular Biological Tools (MBTs) to directly measure contaminant-degrading microorganisms and associated bioremediation processes. Field-scale application of a standardized framework pairing MBTs with traditional contaminant and geochemical analyses was successfully performed at two contaminated sites. At a site with trichloroethene (TCE) impacted groundwater, framework application informed design of an enhanced bioremediation approach. Baseline abundances of 16S rRNA genes for a genus of obligate organohalide-respiring bacteria (i.e., Dehalococcoides) were measured at low abundances (101-102 cells/mL) within the TCE source and plume areas. In combination with geochemical analyses, these data suggested that intrinsic biodegradation (i.e., reductive dechlorination) may be occurring, but activities were limited by electron donor availability. The framework was utilized to support development of a full-scale enhanced bioremediation design (i.e., electron donor addition) and to monitor remedial performance. Additionally, the framework was applied at a second site with residual petroleum hydrocarbon (PHC) impacted soils and groundwater. MBTs, specifically qPCR and 16S gene amplicon rRNA sequencing, were used to characterize intrinsic bioremediation mechanisms. Functional genes associated with anaerobic biodegradation of diesel components (e.g., naphthyl-2-methyl-succinate synthase, naphthalene carboxylase, alkylsuccinate synthase, and benzoyl coenzyme A reductase) were measured to be 2-3 orders of magnitude greater than unimpacted, background samples. Intrinsic bioremediation mechanisms were determined to be sufficient to achieve groundwater remediation objectives. Nonetheless, the framework was further utilized to assess that an enhanced bioremediation could be a successful remedial alternative or complement to source area treatment. While bioremediation of chlorinated solvents, PHCs, and other contaminants has been demonstrated to successfully reduce environmental risk and reach site goals, the application of field-scale MBT data in combination with contaminant and geochemical data analyses to design, implement, and monitor a site-specific bioremediation approach can result in more consistent remedy effectiveness.
Collapse
Affiliation(s)
- Andrew S. Madison
- Golder Associates USA Inc., (Currently WSP USA Inc.), Marlton, NJ, United States,*Correspondence: Andrew S. Madison, ✉
| | - Skyler J. Sorsby
- Golder Associates USA Inc., (Currently WSP USA Inc.), Marlton, NJ, United States
| | | | - Trent A. Key
- ExxonMobil Environmental and Property Solutions Company, Spring, TX, United States
| |
Collapse
|
13
|
Sauk AH, Hug LA. Substrate-restricted methanogenesis and limited volatile organic compound degradation in highly diverse and heterogeneous municipal landfill microbial communities. ISME COMMUNICATIONS 2022; 2:58. [PMID: 37938269 PMCID: PMC9723747 DOI: 10.1038/s43705-022-00141-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/26/2022] [Accepted: 06/14/2022] [Indexed: 06/17/2023]
Abstract
Microbial communities in landfills transform waste and generate methane in an environment unique from other built and natural environments. Landfill microbial diversity has predominantly been observed at the phylum level, without examining the extent of shared organismal diversity across space or time. We used 16S rRNA gene amplicon and shotgun metagenomic sequencing to examine the taxonomic and functional diversity of the microbial communities inhabiting a Southern Ontario landfill. The microbial capacity for volatile organic compound degradation in leachate and groundwater samples was correlated with geochemical conditions. Across the landfill, 25 bacterial and archaeal phyla were present at >1% relative abundance within at least one landfill sample, with Patescibacteria, Bacteroidota, Firmicutes, and Proteobacteria dominating. Methanogens were neither numerous nor particularly abundant, and were predominantly constrained to either acetoclastic or methylotrophic methanogenesis. The landfill microbial community was highly heterogeneous, with 90.7% of organisms present at only one or two sites within this interconnected system. Based on diversity measures, the landfill is a microbial system undergoing a constant state of disturbance and change, driving the extreme heterogeneity observed. Significant differences in geochemistry occurred across the leachate and groundwater wells sampled, with calcium, iron, magnesium, boron, meta and para xylenes, ortho xylenes, and ethylbenzene concentrations contributing most strongly to observed site differences. Predicted microbial degradation capacities indicated a heterogeneous community response to contaminants, including identification of novel proteins implicated in anaerobic degradation of key volatile organic compounds.
Collapse
Affiliation(s)
- Alexandra H Sauk
- Department of Biology, University of Waterloo, 200 University Ave, Waterloo, ON, N2L 3G1, Canada
| | - Laura A Hug
- Department of Biology, University of Waterloo, 200 University Ave, Waterloo, ON, N2L 3G1, Canada.
| |
Collapse
|
14
|
Cabral L, Giovanella P, Pellizzer EP, Teramoto EH, Kiang CH, Sette LD. Microbial communities in petroleum-contaminated sites: Structure and metabolisms. CHEMOSPHERE 2022; 286:131752. [PMID: 34426136 DOI: 10.1016/j.chemosphere.2021.131752] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/24/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Over recent decades, hydrocarbon concentrations have been augmented in soil and water, mainly derived from accidents or operations that input crude oil and petroleum into the environment. Different techniques for remediation have been proposed and used to mitigate oil contamination. Among the available environmental recovery approaches, bioremediation stands out since these hydrocarbon compounds can be used as growth substrates for microorganisms. In turn, microorganisms can play an important role with significant contributions to the stabilization of impacted areas. In this review, we present the current knowledge about responses from natural microbial communities (using DNA barcoding, multiomics, and functional gene markers) and bioremediation experiments (microcosm and mesocosm) conducted in the presence of petroleum and chemical dispersants in different samples, including soil, sediment, and water. Additionally, we present metabolic mechanisms for aerobic/anaerobic hydrocarbon degradation and alternative pathways, as well as a summary of studies showing functional genes and other mechanisms involved in petroleum biodegradation processes.
Collapse
Affiliation(s)
- Lucélia Cabral
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Patricia Giovanella
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Elisa Pais Pellizzer
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Elias Hideo Teramoto
- Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Laboratório de Estudos de Bacias (LEBAC), Departamento de Geologia Aplicada, Instituto de Geociências e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Chang Hung Kiang
- Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Laboratório de Estudos de Bacias (LEBAC), Departamento de Geologia Aplicada, Instituto de Geociências e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Lara Durães Sette
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil.
| |
Collapse
|
15
|
Zhang Z, Guo H, Sun J, Gong X, Wang C, Wang H. Anaerobic phenanthrene biodegradation by a newly isolated sulfate-reducer, strain PheS1, and exploration of the biotransformation pathway. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149148. [PMID: 34311378 DOI: 10.1016/j.scitotenv.2021.149148] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Phenanthrene is a widespread and harmful polycyclic aromatic hydrocarbon that is difficult to anaerobically biodegrade. Current challenges in anaerobic phenanthrene bioremediation are a lack of degrading cultures and limited knowledge of biotransformation pathways. Under sulfate-reducing conditions, pure-cultures and biotransformation processes for anaerobic phenanthrene biodegradation are poorly understood. In this study, strain PheS1, which is phylogenetically closely related to Desulfotomaculum, was found to be a sulfate-reducing phenanthrene-degrading bacterium. Anaerobic phenanthrene biodegradation using PheS1 was proposed based on metabolite and genome analyses, and the initial step was identified as carboxylation based on the detection of 2-phenanthroic acid, [13C]-2-phenanthroic acid, and [D9]-2- phenanthroic acid when phenanthrene+HCO3-, phenanthrene+H13CO3-, and [D10]-phenanthrene+HCO3- were used as the substrate, respectively. PheS1 genome ubiD gene encoding of carboxylase putatively involved in the biodegradation was performed. Next, benzene ring reduction and cleavage that produced benzene compounds and cyclohexane derivative were reported to occur in the downstream biotransformation processes. Additionally, benzene, naphthalene, benz[a]anthracene, and anthracene can be utilised by PheS1, whereas pyrene and benz[a]pyrene cannot. We discovered a new phenanthrene-degrading sulfate-reducer and provided the anaerobic phenanthrene biotransformation pathway under sulfate-reducing conditions, which can act as a reference for practical applications in bioremediation and for studying the molecular mechanisms of phenanthrene in anaerobic zones.
Collapse
Affiliation(s)
- Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Haijiao Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiao Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiaoqiang Gong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Chongyang Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
16
|
McLean JT, Benny A, Nolan MD, Swinand G, Scanlan EM. Cysteinyl radicals in chemical synthesis and in nature. Chem Soc Rev 2021; 50:10857-10894. [PMID: 34397045 DOI: 10.1039/d1cs00254f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nature harnesses the unique properties of cysteinyl radical intermediates for a diverse range of essential biological transformations including DNA biosynthesis and repair, metabolism, and biological photochemistry. In parallel, the synthetic accessibility and redox chemistry of cysteinyl radicals renders them versatile reactive intermediates for use in a vast array of synthetic applications such as lipidation, glycosylation and fluorescent labelling of proteins, peptide macrocyclization and stapling, desulfurisation of peptides and proteins, and development of novel therapeutics. This review provides the reader with an overview of the role of cysteinyl radical intermediates in both chemical synthesis and biological systems, with a critical focus on mechanistic details. Direct insights from biological systems, where applied to chemical synthesis, are highlighted and potential avenues from nature which are yet to be explored synthetically are presented.
Collapse
Affiliation(s)
- Joshua T McLean
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Alby Benny
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Mark D Nolan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Glenna Swinand
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Eoin M Scanlan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| |
Collapse
|
17
|
von Horsten S, Lippert ML, Geisselbrecht Y, Schühle K, Schall I, Essen LO, Heider J. Inactive pseudoenzyme subunits in heterotetrameric BbsCD, a novel short-chain alcohol dehydrogenase involved in anaerobic toluene degradation. FEBS J 2021; 289:1023-1042. [PMID: 34601806 DOI: 10.1111/febs.16216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/16/2021] [Accepted: 09/29/2021] [Indexed: 12/15/2022]
Abstract
Anaerobic toluene degradation proceeds by fumarate addition to produce (R)-benzylsuccinate as first intermediate, which is further degraded via β-oxidation by five enzymes encoded in the conserved bbs operon. This study characterizes two enzymes of this pathway, (E)-benzylidenesuccinyl-CoA hydratase (BbsH), and (S,R)-2-(α-hydroxybenzyl)succinyl-CoA dehydrogenase (BbsCD) from Thauera aromatica. BbsH, a member of the enoyl-CoA hydratase family, converts (E)-benzylidenesuccinyl-CoA to 2-(α-hydroxybenzyl)succinyl-CoA and was subsequently used in a coupled enzyme assay with BbsCD, which belongs to the short-chain dehydrogenases/reductase (SDR) family. The BbsCD crystal structure shows a C2-symmetric heterotetramer consisting of BbsC2 and BbsD2 dimers. BbsD subunits are catalytically active and capable of binding NAD+ and substrate, whereas BbsC subunits represent built-in pseudoenzyme moieties lacking all motifs of the SDR family required for substrate binding or catalysis. Molecular modeling studies predict that the active site of BbsD is specific for conversion of the (S,R)-diastereomer of 2-(α-hydroxybenzyl)succinyl-CoA to (S)-2-benzoylsuccinyl-CoA by hydride transfer to the re-face of nicotinamide adenine dinucleotide (NAD)+ . Furthermore, BbsC subunits are not engaged in substrate binding and merely serve as scaffold for the BbsD dimer. BbsCD represents a novel clade of related enzymes within the SDR family, which adopt a heterotetrameric architecture and catalyze the β-oxidation of aromatic succinate adducts.
Collapse
Affiliation(s)
| | | | | | - Karola Schühle
- Department of Biology, Philipps-Universität, Marburg, Germany
| | - Iris Schall
- Department of Biology, Philipps-Universität, Marburg, Germany
| | | | - Johann Heider
- Department of Biology, Philipps-Universität, Marburg, Germany
| |
Collapse
|
18
|
Wang B, Kuang S, Shao H, Wang L, Wang H. Anaerobic-petroleum degrading bacteria: Diversity and biotechnological applications for improving coastal soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 224:112646. [PMID: 34399124 DOI: 10.1016/j.ecoenv.2021.112646] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Due to the industrial emissions and accidental spills, the critical material for modern industrial society petroleum pollution causes severe ecological damage. The prosperous oil exploitation and transportation causes the recalcitrant, hazardous, and carcinogenic sludge widespread in the coastal wetlands. The costly physicochemical-based remediation remains the secondary and inadequate treatment for the derivatives along with the tailings. Anaerobic microbial petroleum degrading biotechnology has received extensive attention for its cost acceptable, eco-friendly, and fewer health hazards. As a result of the advances in biotechnology and microbiology, the anaerobic oil-degrading bacteria have been well developing to achieve the same remediation effects with lower operating costs. This review summarizes the advantages and potential scenarios of the anaerobic degrading bacteria, such as sulfate-reducing bacteria, denitrifying bacteria, and metal-reducing bacteria in the coastal area decomposing the alkanes, alkenes, aromatic hydrocarbons, polycyclic aromatic, and related derivatives. In the future, a complete theoretical basis of microbiological biotechnology, molecular biology, and electrochemistry is necessary to make efficient and environmental-friendly use of anaerobic degradation bacteria to mineralize oil sludge organic wastes.
Collapse
Affiliation(s)
- Bingchen Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Shaoping Kuang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China.
| | - Hongbo Shao
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China; Institute of Agriculture Resources and Environment, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing 210014, PR China; Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224002, China.
| | - Lei Wang
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Huihui Wang
- College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| |
Collapse
|
19
|
Sengupta K, Pal S. A review on microbial diversity and genetic markers involved in methanogenic degradation of hydrocarbons: futuristic prospects of biofuel recovery from contaminated regions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:40288-40307. [PMID: 33844144 DOI: 10.1007/s11356-021-13666-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Microbial activities within oil reservoirs have adversely impacted the world's majority of oil by lowering its quality, thereby increasing its recovery and refining cost. Moreover, conventional method of extraction leaves behind nearly two-thirds of the fossil fuels in the oil fields. This huge potential can be extracted if engineered methanogenic consortium is adapted to convert the hydrocarbons into natural gas. This process involves conversion of crude oil hydrocarbons into methanogenic substrates by syntrophic and fermentative bacteria, which are subsequently utilized by methanogens to produce methane. Microbial diversity of such environments supports the viability of this process. This review illuminates the potentials of abundant microbial groups such as Syntrophaceae, Anaerolineaceae, Clostridiales and Euryarchaeota in petroleum hydrocarbon-related environment, their genetic markers, biochemical process and omics-based bioengineering methods involved in methane generation. Increase in the copy numbers of catabolic genes during methanogenesis highlights the prospect of developing engineered biofuel recovery technology. Several lab-based methanogenic consortia from depleted petroleum reservoirs and microcosm studies so far would not be enough for field application without the advent of multi-omics-based technologies to trawl out the bottleneck parameters of the enhanced fuel recovery process. The adaptability of efficient consortium of versatile hydrocarbonoclastic and methanogenic microorganisms under environmental stress conditions is further needed to be investigated. The improved process might hold the potential of methane extraction from petroleum waste like oil tank and refinery sludge, oil field deposits, etc. What sounds as biodegradation could be a beginning of converting waste into wealth by recovery of stranded energy assets.
Collapse
Affiliation(s)
- Kriti Sengupta
- Bioenergy Group, Agharkar Research Institute, Pune, 411004, India
| | - Siddhartha Pal
- National Centre for Cell Science, Ganeshkhind, Pune, 411007, India.
| |
Collapse
|
20
|
Zhang Z, Sun J, Guo H, Gong X, Wang C, Wang H. Investigation of anaerobic biodegradation of phenanthrene by a sulfate-dependent Geobacter sulfurreducens strain PheS2. JOURNAL OF HAZARDOUS MATERIALS 2021; 409:124522. [PMID: 33229262 DOI: 10.1016/j.jhazmat.2020.124522] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 06/11/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous and harmful contaminants, which can be degraded aerobically. However, the persistence of PAHs in anoxic environments indicates that anaerobic biodegradation of PAHs should also be investigated. Pure-culture and biotransformation processes for anaerobic phenanthrene biodegradation with sulfate as a terminal electron acceptor remains in its infancy. In this study, we investigated anaerobic biodegradation of PAHs by PheS2, an isolated phenanthrene-utilizing sulfate-reducer, using phenanthrene as a model compound. PheS2 was phylogenetically closely related to Geobacter sulfurreducens and reduced sulfate to sulfide during anaerobic phenanthrene biodegradation. Phenanthrene biodegradation processes were detected using gas chromatography-mass spectrometry, genome, and reverse transcription quantitative PCR analyses. Carboxylation was the initial step of anaerobic phenanthrene biodegradation based upon detection of 2- and 4-phenanthroic acid, its isotopically labeled analogs when using 13C-labeled bicarbonate and fully deuterated-phenanthrene (C14D10), and genes encoding enzymes putatively involved in the biodegradation. Further, ring-system reducing and cleavage occurred, and substituted benzene series and cyclohexane derivatives were detected in downstream biotransformation metabolites. Additionally, PheS2 can degrade benzene, naphthalene, anthracene, and benz[a]anthracene, but not pyrene and benz[a]pyrene. This study describes the isolation of an anaerobic phenanthrene-degrading sulfate-reducer, the first pure-culture evidence of phenanthrene biotransformation processes with sulfate as an electron acceptor.
Collapse
Affiliation(s)
- Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiao Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Haijiao Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiaoqiang Gong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Chongyang Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
21
|
Salii I, Szaleniec M, Zein AA, Seyhan D, Sekuła A, Schühle K, Kaplieva-Dudek I, Linne U, Meckenstock RU, Heider J. Determinants for Substrate Recognition in the Glycyl Radical Enzyme Benzylsuccinate Synthase Revealed by Targeted Mutagenesis. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04954] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Iryna Salii
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, 35043 Marburg, Germany
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science, 30-239 Kraków, Poland
| | - Ammar Alhaj Zein
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, 35043 Marburg, Germany
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Deniz Seyhan
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, 35043 Marburg, Germany
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Anna Sekuła
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science, 30-239 Kraków, Poland
| | - Karola Schühle
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, 35043 Marburg, Germany
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | | | - Uwe Linne
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Philipps University Marburg, 35043 Marburg, Germany
| | | | - Johann Heider
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, 35043 Marburg, Germany
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| |
Collapse
|
22
|
Zhang Z, Guo H, Sun J, Gong X, Wang C, Wang H. Exploration of the biotransformation processes in the biodegradation of phenanthrene by a facultative anaerobe, strain PheF2, with Fe(III) or O 2 as an electron acceptor. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 750:142245. [PMID: 33182168 DOI: 10.1016/j.scitotenv.2020.142245] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/01/2020] [Accepted: 09/04/2020] [Indexed: 06/11/2023]
Abstract
The study of biodegradation of polycyclic aromatic hydrocarbons (PAHs) with metal ions as electron acceptors is still in its infancy. Here, a pure culture of PheF2 sharing 99.79% 16S rRNA-sequence similarity with Trichococcus alkaliphilus, which was recently reported to degrade PAHs, was isolated and found to degrade PAHs with Fe (III) or O2 reduction. Phenanthrene was selected as a model of PAH to study the biodegradation process by PheF2 with Fe (III) or O2 as an electron acceptor. PheF2 exhibited nearly 100%, 37.1%, and 28.5% anaerobic biodegradation of phenanthrene at initial concentrations of 280.7 μM, 280.6 μM, and 281.3 μM, respectively, within 10 days under anaerobic conditions with XAD-7 as a carrier, heptamethylnonane (HMN) as a solution, and nothing, respectively. PheF2 could degrade nearly 100% of the initial phenanthrene concentration of 283.4 μM under aerobic conditions within three days. The initial step of phenanthrene biodegradation by PheF2 involved carboxylation and dioxygenation under anaerobic and aerobic conditions, respectively. The biotransformation processes of phenanthrene degradation by PheF2 with Fe(III) or O2 as an electron acceptor were explored by metabolite and genome analysis. These findings provide an important theoretical support for evaluation of PAHs fate and for PAHs pollution control or remediation in anaerobic and aerobic environments.
Collapse
Affiliation(s)
- Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Haijiao Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiao Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiaoqiang Gong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Chongyang Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
23
|
Laczi K, Erdeiné Kis Á, Szilágyi Á, Bounedjoum N, Bodor A, Vincze GE, Kovács T, Rákhely G, Perei K. New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era. Front Microbiol 2020; 11:590049. [PMID: 33304336 PMCID: PMC7701123 DOI: 10.3389/fmicb.2020.590049] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
The accumulation of petroleum hydrocarbons in the environment substantially endangers terrestrial and aquatic ecosystems. Many microbial strains have been recognized to utilize aliphatic and aromatic hydrocarbons under aerobic conditions. Nevertheless, most of these pollutants are transferred by natural processes, including rain, into the underground anaerobic zones where their degradation is much more problematic. In oxic zones, anaerobic microenvironments can be formed as a consequence of the intensive respiratory activities of (facultative) aerobic microbes. Even though aerobic bioremediation has been well-characterized over the past few decades, ample research is yet to be done in the field of anaerobic hydrocarbon biodegradation. With the emergence of high-throughput techniques, known as omics (e.g., genomics and metagenomics), the individual biodegraders, hydrocarbon-degrading microbial communities and metabolic pathways, interactions can be described at a contaminated site. Omics approaches provide the opportunity to examine single microorganisms or microbial communities at the system level and elucidate the metabolic networks, interspecies interactions during hydrocarbon mineralization. Metatranscriptomics and metaproteomics, for example, can shed light on the active genes and proteins and functional importance of the less abundant species. Moreover, novel unculturable hydrocarbon-degrading strains and enzymes can be discovered and fit into the metabolic networks of the community. Our objective is to review the anaerobic hydrocarbon biodegradation processes, the most important hydrocarbon degraders and their diverse metabolic pathways, including the use of various terminal electron acceptors and various electron transfer processes. The review primarily focuses on the achievements obtained by the current high-throughput (multi-omics) techniques which opened new perspectives in understanding the processes at the system level including the metabolic routes of individual strains, metabolic/electric interaction of the members of microbial communities. Based on the multi-omics techniques, novel metabolic blocks can be designed and used for the construction of microbial strains/consortia for efficient removal of hydrocarbons in anaerobic zones.
Collapse
Affiliation(s)
- Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Ágnes Erdeiné Kis
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Naila Bounedjoum
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Attila Bodor
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | | | - Tamás Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Katalin Perei
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| |
Collapse
|
24
|
Krolicka A, Gomiero A, Baussant T. qPCR-based assessment of microfaunal indicators of oil for monitoring benthos around oil and gas platforms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 736:139527. [PMID: 32497879 DOI: 10.1016/j.scitotenv.2020.139527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/05/2020] [Accepted: 05/16/2020] [Indexed: 06/11/2023]
Abstract
Today's benthic offshore biological monitoring of oil & gas (O&G) activities relies on macrofauna taxa enumeration. For the future, analysis of DNA isolated directly from sediments holds great potential for multi-trophic biodiversity surveys and the monitoring of a larger spectrum of benthic taxa, including micro-fauna. Here, we evaluate more specifically the potential of microfauna-specific gene quantification in relation to both petroleum-related discharge compounds and other seafloor environmental properties. We carried out this evaluation using sediment samples collected at drilling Region III on the Norwegian continental shelf where DNA metabarcoding of eukaryotic diversity was already performed. Generally, the quantification of microfauna indicator taxa related well to the gradient of contamination on the seafloor. Contrary to eukaryotic Euplotida, metabarcoding data and qPCR numbers for indicative prokaryotic taxa showed the same relationship to offshore contaminants (both showed positive relationship). We found absolute numbers of SSU rRNA gene copies of (1) Dinophyceae, Bacillariophyceae and Alcanivorax were correlated with the level of petroleum-related compounds but not with other environmental variables, (2) bacteria closely related to Shewanella were correlated with the concentration of Ba, PAH, as well to percent of gravel, (3) Desulfobacteriales correlated with petroleum-related contaminants, but as well with percent of gravel and grain size. Findings from our study suggest that biomonitoring surveys of O&G activities on benthos could benefit from quantification of specific micro-fauna indicators that is simpler and faster than the methods currently used for impact assessment of benthos.
Collapse
Affiliation(s)
- Adriana Krolicka
- NORCE - Norwegian Research Centre - Environment, Mekjarvik 12, 4070 Randaberg, Norway.
| | - Alessio Gomiero
- NORCE - Norwegian Research Centre - Environment, Mekjarvik 12, 4070 Randaberg, Norway
| | - Thierry Baussant
- NORCE - Norwegian Research Centre - Environment, Mekjarvik 12, 4070 Randaberg, Norway
| |
Collapse
|
25
|
Zhang Z, Sun J, Guo H, Wang C, Fang T, Rogers MJ, He J, Wang H. Anaerobic biodegradation of phenanthrene by a newly isolated nitrate-dependent Achromobacter denitrificans strain PheN1 and exploration of the biotransformation processes by metabolite and genome analyses. Environ Microbiol 2020; 23:908-923. [PMID: 32812321 DOI: 10.1111/1462-2920.15201] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/15/2020] [Indexed: 11/29/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widespread and harmful contaminants and are more persistent under anaerobic conditions. The bioremediation of PAHs in anaerobic zones has been enhanced by treating the contamination with nitrate, which is thermodynamically favourable, cost-effective, and highly soluble. However, anaerobic PAHs biotransformation processes that employ nitrate as an electron acceptor have not been fully explored. In this study, we investigated the anaerobic biotransformation of PAHs by strain PheN1, a newly isolated phenanthrene-degrading denitrifier, using phenanthrene as a model compound. PheN1 is phylogenetically closely related to Achromobacter denitrificans and reduces nitrate to nitrite (not N2 ) during the anaerobic phenanthrene degradation process. Phenanthrene biotransformation processes were detected using gas chromatography-mass spectrometry and were further examined by reverse transcription-quantitative PCR and genome analyses. Carboxylation and methylation were both found to be the initial steps in the phenanthrene degradation process. Downstream biotransformation processed benzene compounds and cyclohexane derivatives. This study describes the isolation of an anaerobic phenanthrene-degrading bacterium along with the pure-culture evidence of phenanthrene biotransformation processes with nitrate as an electron acceptor. The findings in this study can improve our understanding of anaerobic PAHs biodegradation processes and guide PAHs bioremediation by adding nitrate to anaerobic environments.
Collapse
Affiliation(s)
- Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jiao Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Haijiao Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Chongyang Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Tingting Fang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Matthew J Rogers
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| |
Collapse
|
26
|
Momper L, Semler A, Lu GS, Miyazaki M, Imachi H, Amend JP. Rectinema subterraneum sp. nov, a chemotrophic spirochaete isolated from the deep terrestrial subsurface. Int J Syst Evol Microbiol 2020; 70:4739-4747. [PMID: 32730198 DOI: 10.1099/ijsem.0.004339] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, obligately anaerobic bacterium (strain SURF-ANA1T) was isolated from deep continental subsurface fluids at a depth of 1500 m below surface in the former Homestake Gold Mine (now Sanford Underground Research Facility, in Lead, South Dakota, USA). Cells of strain SURF-ANA1T were Gram-negative, helical, non-spore-forming and were 0.25-0.55×5.0-75.0 µm with a wavelength of 0.5-0.62 µm. Strain SURF-ANA1T grew at 15-50 °C (optimally at 40 °C), at pH 4.8-9.0 (pH 7.2) and in 1.0-40.0 g l-1 NaCl (10 g l-1 NaCl). The strain grew chemoheterotrophically with hydrogen or mono-, di- and polysaccharides as electron donors. The major cellular fatty acids in order of decreasing abundance (comprising >5% of total) were 10-methyl C16:0, iso-C15:0, C18:2 and C18:0 dimethyl acetal (DMA) and C20:0 methylene-nonadecanoic acid. Phylogenetic analysis based on the 16S rRNA gene sequence of strain SURF-ANA1T indicated a closest relationship with the recently characterized Rectinema cohabitans (99%). Despite high sequence identity, because of its distinct physiology, morphology and fatty acid profile, strain SURF-ANA1T is considered to represent a novel species within the genus Rectinema, for which the name Rectinema subterraneum sp. nov. is proposed. To our knowledge, this is the first report of an isolate within the phylum Spirochaetes from the deep (>100 m) terrestrial subsurface. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and genomic sequences of strain SURF-ANA1T are KU359248 and GCF 009768935.1, respectively. The type strain of Rectinema subterraneum is SURF-ANA1T (=ATCC TSD-67=JCM 32656).
Collapse
Affiliation(s)
- Lily Momper
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, USA.,Exponent Inc. 1055 East Colorado Blvd, Pasadena, CA, USA
| | - Amanda Semler
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Guang Sin Lu
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Masayuki Miyazaki
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Hiroyuki Imachi
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA.,Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
27
|
Dhar K, Subashchandrabose SR, Venkateswarlu K, Krishnan K, Megharaj M. Anaerobic Microbial Degradation of Polycyclic Aromatic Hydrocarbons: A Comprehensive Review. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2020; 251:25-108. [PMID: 31011832 DOI: 10.1007/398_2019_29] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a class of hazardous organic contaminants that are widely distributed in nature, and many of them are potentially toxic to humans and other living organisms. Biodegradation is the major route of detoxification and removal of PAHs from the environment. Aerobic biodegradation of PAHs has been the subject of extensive research; however, reports on anaerobic biodegradation of PAHs are so far limited. Microbial degradation of PAHs under anaerobic conditions is difficult because of the slow growth rate of anaerobes and low energy yield in the metabolic processes. Despite the limitations, some anaerobic bacteria degrade PAHs under nitrate-reducing, sulfate-reducing, iron-reducing, and methanogenic conditions. Anaerobic biodegradation, though relatively slow, is a significant process of natural attenuation of PAHs from the impacted anoxic environments such as sediments, subsurface soils, and aquifers. This review is intended to provide comprehensive details on microbial degradation of PAHs under various reducing conditions, to describe the degradation mechanisms, and to identify the areas that should receive due attention in further investigations.
Collapse
Affiliation(s)
- Kartik Dhar
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
- Department of Microbiology, University of Chittagong, Chittagong, Bangladesh
| | - Suresh R Subashchandrabose
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, India
| | - Kannan Krishnan
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia.
| |
Collapse
|
28
|
Ye Q, Liang C, Chen X, Fang T, Wang Y, Wang H. Molecular characterization of methanogenic microbial communities for degrading various types of polycyclic aromatic hydrocarbon. J Environ Sci (China) 2019; 86:97-106. [PMID: 31787194 DOI: 10.1016/j.jes.2019.04.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 06/10/2023]
Abstract
Knowledge on methanogenic microbial communities associated with the degradation of polycyclic aromatic hydrocarbons (PAHs) is crucial to developing strategies for PAHs bioremediation. In this study, the linkage between the type of PAHs and microbial community structure was fully investigated through 16S rRNA gene sequencing on four PAH-degrading cultures. Putative degradation products were also detected. Our results indicated that naphthalene (Nap)/2-methylnaphthalene (2-Nap), phenanthrene (Phe) and anthracene (Ant) sculpted different microbial communities. Among them, Nap and 2-Nap selected for similar degrading bacteria (i.e., Alicycliphilus and Thauera) and methanogens (Methanomethylovorans and Methanobacterium). Nap and 2-Nap were probably activated via carboxylation, producing 2-naphthoic acid. In contrast, Phe and Ant shaped different bacterial and archaeal communities, with Arcobacter and Acinetobacter being Phe-degraders and Thiobacillus Ant-degrader. Methanogenic archaea Methanobacterium and Methanomethylovorans predominated Phe-degrading and Ant-degrading culture, respectively. These findings can improve our understanding of natural PAHs attenuation and provide some guidance for PAHs bioremediation in methanogenic environment.
Collapse
Affiliation(s)
- Quanhui Ye
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Chengyue Liang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xunwen Chen
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology of China, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Tingting Fang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yun Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
29
|
Rossmassler K, Snow CD, Taggart D, Brown C, De Long SK. Advancing biomarkers for anaerobic o-xylene biodegradation via metagenomic analysis of a methanogenic consortium. Appl Microbiol Biotechnol 2019; 103:4177-4192. [PMID: 30968165 DOI: 10.1007/s00253-019-09762-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/07/2019] [Accepted: 03/10/2019] [Indexed: 10/27/2022]
Abstract
Quantifying functional biomarker genes and their transcripts provides critical lines of evidence for contaminant biodegradation; however, accurate quantification depends on qPCR primers that contain no, or minimal, mismatches with the target gene. Developing accurate assays has been particularly challenging for genes encoding fumarate-adding enzymes (FAE) due to the high level of genetic diversity in this gene family. In this study, metagenomics applied to a field-derived, o-xylene-degrading methanogenic consortium revealed genes encoding FAE that would not be accurately quantifiable by any previously available PCR assays. Sequencing indicated that a gene similar to the napthylmethylsuccinate synthase gene (nmsA) was most abundant, although benzylsuccinate synthase genes (bssA) also were present along with genes encoding alkylsuccinate synthase (assA). Upregulation of the nmsA-like gene was observed during o-xylene degradation. Protein homology modeling indicated that mutations in the active site, relative to a BssA that acts on toluene, increase binding site volume and accessibility, potentially to accommodate the relatively larger o-xylene. The new nmsA-like gene was also detected at substantial concentrations at field sites with a history of xylene contamination.
Collapse
Affiliation(s)
- Karen Rossmassler
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, USA.,Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Christopher D Snow
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | | | - Casey Brown
- Microbial Insights, Inc., Knoxville, TN, USA
| | - Susan K De Long
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, USA.
| |
Collapse
|
30
|
Identification of naphthalene carboxylase subunits of the sulfate-reducing culture N47. Biodegradation 2019; 30:147-160. [DOI: 10.1007/s10532-019-09872-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 02/26/2019] [Indexed: 11/26/2022]
|
31
|
Jochum LM, Schreiber L, Marshall IPG, Jørgensen BB, Schramm A, Kjeldsen KU. Single-Cell Genomics Reveals a Diverse Metabolic Potential of Uncultivated Desulfatiglans-Related Deltaproteobacteria Widely Distributed in Marine Sediment. Front Microbiol 2018; 9:2038. [PMID: 30233524 PMCID: PMC6129605 DOI: 10.3389/fmicb.2018.02038] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/13/2018] [Indexed: 11/13/2022] Open
Abstract
Desulfatiglans-related organisms comprise one of the most abundant deltaproteobacterial lineages in marine sediments where they occur throughout the sediment column in a gradient of increasing sulfate and organic carbon limitation with depth. Characterized Desulfatiglans isolates are dissimilatory sulfate reducers able to grow by degrading aromatic hydrocarbons. The ecophysiology of environmental Desulfatiglans-populations is poorly understood, however, possibly utilization of aromatic compounds may explain their predominance in marine subsurface sediments. We sequenced and analyzed seven Desulfatiglans-related single-cell genomes (SAGs) from Aarhus Bay sediments to characterize their metabolic potential with regard to aromatic compound degradation and energy metabolism. The average genome assembly size was 1.3 Mbp and completeness estimates ranged between 20 and 50%. Five of the SAGs (group 1) originated from the sulfate-rich surface part of the sediment while two (group 2) originated from sulfate-depleted subsurface sediment. Based on 16S rRNA gene amplicon sequencing group 2 SAGs represent the more frequent types of Desulfatiglans-populations in Aarhus Bay sediments. Genes indicative of aromatic compound degradation could be identified in both groups, but the two groups were metabolically distinct with regard to energy conservation. Group 1 SAGs carry a full set of genes for dissimilatory sulfate reduction, whereas the group 2 SAGs lacked any genetic evidence for sulfate reduction. The latter may be due to incompleteness of the SAGs, but as alternative energy metabolisms group 2 SAGs carry the genetic potential for growth by acetogenesis and fermentation. Group 1 SAGs encoded reductive dehalogenase genes, allowing them to access organohalides and possibly conserve energy by their reduction. Both groups possess sulfatases unlike their cultured relatives allowing them to utilize sulfate esters as source of organic carbon and sulfate. In conclusion, the uncultivated marine Desulfatiglans populations are metabolically diverse, likely reflecting different strategies for coping with energy and sulfate limitation in the subsurface seabed.
Collapse
Affiliation(s)
- Lara M Jochum
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Lars Schreiber
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Ian P G Marshall
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Bo B Jørgensen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| |
Collapse
|
32
|
Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture. Microorganisms 2018; 6:microorganisms6030065. [PMID: 29996505 PMCID: PMC6164631 DOI: 10.3390/microorganisms6030065] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/02/2018] [Accepted: 07/08/2018] [Indexed: 11/23/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAH) such as naphthalene are widespread, recalcitrant pollutants in anoxic and methanogenic environments. A mechanism catalyzing PAH activation under methanogenic conditions has yet to be discovered, and the microbial communities coordinating their metabolism are largely unknown. This is primarily due to the difficulty of cultivating PAH degraders, requiring lengthy incubations to yield sufficient biomass for biochemical analysis. Here, we sought to characterize a new methanogenic naphthalene-degrading enrichment culture using DNA-based stable isotope probing (SIP) and metagenomic analyses. 16S rRNA gene sequencing of fractionated DNA pinpointed an unclassified Clostridiaceae species as a putative naphthalene degrader after two months of SIP incubation. This finding was supported by metabolite and metagenomic evidence of genes predicted to encode for enzymes facilitating naphthalene carboxylic acid CoA-thioesterification and degradation of an unknown arylcarboxyl-CoA structure. Our findings also suggest a possible but unknown role for Desulfuromonadales in naphthalene degradation. This is the first reported functional evidence of PAH biodegradation by a methanogenic consortium, and we envision that this approach could be used to assess carbon flow through other slow growing enrichment cultures and environmental samples.
Collapse
|
33
|
Fermentative Spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats. ISME JOURNAL 2018; 12:2039-2050. [PMID: 29849169 PMCID: PMC6052044 DOI: 10.1038/s41396-018-0148-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 03/23/2018] [Accepted: 03/29/2018] [Indexed: 11/08/2022]
Abstract
Spirochaetes are frequently detected in anoxic hydrocarbon- and organohalide-polluted groundwater, but their role in such ecosystems has remained unclear. To address this, we studied a sulfate-reducing, naphthalene-degrading enrichment culture, mainly comprising the sulfate reducer Desulfobacterium N47 and the rod-shaped Spirochete Rectinema cohabitans HM. Genome sequencing and proteome analysis suggested that the Spirochete is an obligate fermenter that catabolizes proteins and carbohydrates, resulting in acetate, ethanol, and molecular hydrogen (H2) production. Physiological experiments inferred that hydrogen is an important link between the two bacteria in the enrichment culture, with H2 derived from fermentation by R. cohabitans used as reductant for sulfate reduction by Desulfobacterium N47. Differential proteomics and physiological experiments showed that R. cohabitans utilizes biomass (proteins and carbohydrates) released from dead cells of Desulfobacterium N47. Further comparative and community genome analyses indicated that other Rectinema phylotypes are widespread in contaminated environments and may perform a hydrogenogenic fermentative lifestyle similar to R. cohabitans. Together, these findings indicate that environmental Spirochaetes scavenge detrital biomass and in turn drive necromass recycling at anoxic hydrocarbon-contaminated sites and potentially other habitats.
Collapse
|
34
|
Toth CRA, Gieg LM. Time Course-Dependent Methanogenic Crude Oil Biodegradation: Dynamics of Fumarate Addition Metabolites, Biodegradative Genes, and Microbial Community Composition. Front Microbiol 2018; 8:2610. [PMID: 29354103 PMCID: PMC5758579 DOI: 10.3389/fmicb.2017.02610] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/14/2017] [Indexed: 11/13/2022] Open
Abstract
Biodegradation of crude oil in subsurface petroleum reservoirs has adversely impacted most of the world's oil, converting this resource to heavier forms that are of lower quality and more challenging to recover. Oil degradation in deep reservoir environments has been attributed to methanogenesis over geological time, yet our understanding of the processes and organisms mediating oil transformation in the absence of electron acceptors remains incomplete. Here, we sought to identify hydrocarbon activation mechanisms and reservoir-associated microorganisms that may have helped shape the formation of biodegraded oil by incubating oilfield produced water in the presence of light (°API = 32) or heavy crude oil (°API = 16). Over the course of 17 months, we conducted routine analytical (GC, GC-MS) and molecular (PCR/qPCR of assA and bssA genes, 16S rRNA gene sequencing) surveys to assess microbial community composition and activity changes over time. Over the incubation period, we detected the formation of transient hydrocarbon metabolites indicative of alkane and alkylbenzene addition to fumarate, corresponding with increases in methane production and fumarate addition gene abundance. Chemical and gene-based evidence of hydrocarbon biodegradation under methanogenic conditions was supported by the enrichment of hydrocarbon fermenters known to catalyze fumarate addition reactions (e.g., Desulfotomaculum, Smithella), along with syntrophic bacteria (Syntrophus), methanogenic archaea, and several candidate phyla (e.g., “Atribacteria”, “Cloacimonetes”). Our results reveal that fumarate addition is a possible mechanism for catalyzing the methanogenic biodegradation of susceptible saturates and aromatic hydrocarbons in crude oil, and we propose the roles of community members and candidate phyla in our cultures that may be involved in hydrocarbon transformation to methane in crude oil systems.
Collapse
Affiliation(s)
- Courtney R A Toth
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Lisa M Gieg
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
35
|
Dong X, Jochmann MA, Elsner M, Meyer AH, Bäcker LE, Rahmatullah M, Schunk D, Lens G, Meckenstock RU. Monitoring Microbial Mineralization Using Reverse Stable Isotope Labeling Analysis by Mid-Infrared Laser Spectroscopy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:11876-11883. [PMID: 28903553 PMCID: PMC5647565 DOI: 10.1021/acs.est.7b02909] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Assessing the biodegradation of organic compounds is a frequent question in environmental science. Here, we present a sensitive, inexpensive, and simple approach to monitor microbial mineralization using reverse stable isotope labeling analysis (RIL) of dissolved inorganic carbon (DIC). The medium for the biodegradation assay contains regular organic compounds and 13C-labeled DIC with 13C atom fractions (x(13C)DIC) higher than natural abundance (typically 2-50%). The produced CO2 (x(13C) ≈ 1.11%) gradually dilutes the initial x(13C)DIC allowing to quantify microbial mineralization using mass-balance calculations. For 13C-enriched CO2 samples, a newly developed isotope ratio mid-infrared spectrometer was introduced with a precision of x(13C) < 0.006%. As an example for extremely difficult and slowly degradable compounds, CO2 production was close to the theoretical stoichiometry for anaerobic naphthalene degradation by a sulfate-reducing enrichment culture. Furthermore, we could measure the aerobic degradation of dissolved organic carbon (DOC) adsorbed to granular activated carbon in a drinking water production plant, which cannot be labeled with 13C. Thus, the RIL approach can be applied to sensitively monitor biodegradation of various organic compounds under anoxic or oxic conditions.
Collapse
Affiliation(s)
- Xiyang Dong
- Biofilm
Centre, University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
| | - Maik A. Jochmann
- Instrumental
Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Martin Elsner
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, D-81377 Munich, Germany
| | - Armin H. Meyer
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
| | - Leonard E. Bäcker
- Biofilm
Centre, University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Mona Rahmatullah
- Biofilm
Centre, University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Daniel Schunk
- RWW Rheinisch-Westfälische
Wasserwerksgesellschaft mbH, Am Schloß
Broich 1-3, 45479 Mülheim an der Ruhr, Germany
| | - Guido Lens
- RWW Rheinisch-Westfälische
Wasserwerksgesellschaft mbH, Am Schloß
Broich 1-3, 45479 Mülheim an der Ruhr, Germany
| | - Rainer U. Meckenstock
- Biofilm
Centre, University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
- Phone: +49 (201) 183-6601; fax: +49 (201) 183-6603; e-mail:
| |
Collapse
|
36
|
Backman LRF, Funk MA, Dawson CD, Drennan CL. New tricks for the glycyl radical enzyme family. Crit Rev Biochem Mol Biol 2017; 52:674-695. [PMID: 28901199 DOI: 10.1080/10409238.2017.1373741] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Glycyl radical enzymes (GREs) are important biological catalysts in both strict and facultative anaerobes, playing key roles both in the human microbiota and in the environment. GREs contain a backbone glycyl radical that is post-translationally installed, enabling radical-based mechanisms. GREs function in several metabolic pathways including mixed acid fermentation, ribonucleotide reduction and the anaerobic breakdown of the nutrient choline and the pollutant toluene. By generating a substrate-based radical species within the active site, GREs enable C-C, C-O and C-N bond breaking and formation steps that are otherwise challenging for nonradical enzymes. Identification of previously unknown family members from genomic data and the determination of structures of well-characterized GREs have expanded the scope of GRE-catalyzed reactions as well as defined key features that enable radical catalysis. Here, we review the structures and mechanisms of characterized GREs, classifying members into five categories. We consider the open questions about each of the five GRE classes and evaluate the tools available to interrogate uncharacterized GREs.
Collapse
Affiliation(s)
- Lindsey R F Backman
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Michael A Funk
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA.,b Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , IL , USA
| | - Christopher D Dawson
- c Department of Biology , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Catherine L Drennan
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA.,c Department of Biology , Massachusetts Institute of Technology , Cambridge , MA , USA.,d Howard Hughes Medical Institute , Massachusetts Institute of Technology , Cambridge , MA , USA
| |
Collapse
|
37
|
Michas A, Vestergaard G, Trautwein K, Avramidis P, Hatzinikolaou DG, Vorgias CE, Wilkes H, Rabus R, Schloter M, Schöler A. More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis. MICROBIOME 2017; 5:118. [PMID: 28893308 PMCID: PMC5594585 DOI: 10.1186/s40168-017-0337-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/03/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Natural oil seeps offer the opportunity to study the adaptation of ecosystems and the associated microbiota to long-term oil exposure. In the current study, we investigated a land-to-sea transition ecosystem called "Keri Lake" in Zakynthos Island, Greece. This ecosystem is unique due to asphalt oil springs found at several sites, a phenomenon already reported 2500 years ago. Sediment microbiomes at Keri Lake were studied, and their structure and functional potential were compared to other ecosystems with oil exposure histories of various time periods. RESULTS Replicate sediment cores (up to 3-m depth) were retrieved from one site exposed to oil as well as a non-exposed control site. Samples from three different depths were subjected to chemical analysis and metagenomic shotgun sequencing. At the oil-exposed site, we observed high amounts of asphalt oil compounds and a depletion of sulfate compared to the non-exposed control site. The numbers of reads assigned to genes involved in the anaerobic degradation of hydrocarbons were similar between the two sites. The numbers of denitrifiers and sulfate reducers were clearly lower in the samples from the oil-exposed site, while a higher abundance of methanogens was detected compared to the non-exposed site. Higher abundances of the genes of methanogenesis were also observed in the metagenomes from other ecosystems with a long history of oil exposure, compared to short-term exposed environments. CONCLUSIONS The analysis of Keri Lake metagenomes revealed that microbiomes in the oil-exposed sediment have a higher potential for methanogenesis over denitrification/sulfate reduction, compared to those in the non-exposed site. Comparison with metagenomes from various oil-impacted environments suggests that syntrophic interactions of hydrocarbon degraders with methanogens are favored in the ecosystems with a long-term presence of oil.
Collapse
Affiliation(s)
- Antonios Michas
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Kathleen Trautwein
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Pavlos Avramidis
- Department of Geology, University of Patras, Panepistimioupoli Patron, 26504 Rio-Patras, Greece
| | - Dimitris G. Hatzinikolaou
- Department of Biology, National and Kapodistrian University of Athens, Zografou University Campus, 15784 Athens, Greece
| | - Constantinos E. Vorgias
- Department of Biology, National and Kapodistrian University of Athens, Zografou University Campus, 15784 Athens, Greece
| | - Heinz Wilkes
- Organic Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Anne Schöler
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| |
Collapse
|
38
|
Weyrauch P, Zaytsev AV, Stephan S, Kocks L, Schmitz OJ, Golding BT, Meckenstock RU. Conversion of cis-2-carboxycyclohexylacetyl-CoA in the downstream pathway of anaerobic naphthalene degradation. Environ Microbiol 2017; 19:2819-2830. [PMID: 28574200 DOI: 10.1111/1462-2920.13806] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/23/2017] [Accepted: 05/27/2017] [Indexed: 11/29/2022]
Abstract
The cyclohexane derivative cis-2-(carboxymethyl)cyclohexane-1-carboxylic acid [(1R,2R)-/(1S,2S)-2-(carboxymethyl)cyclohexane-1-carboxylic acid] has previously been identified as metabolite in the pathway of anaerobic degradation of naphthalene by sulfate-reducing bacteria. We tested the corresponding CoA esters of isomers and analogues of this compound for conversion in cell free extracts of the anaerobic naphthalene degraders Desulfobacterium strain N47 and Deltaproteobacterium strain NaphS2. Conversion was only observed for the cis-isomer, verifying that this is a true intermediate and not a dead-end product. Mass-spectrometric analyses confirmed that conversion is performed by an acyl-CoA dehydrogenase and a subsequent hydratase yielding an intermediate with a tertiary hydroxyl-group. We propose that a novel kind of ring-opening lyase is involved in the further catabolic pathway proceeding via pimeloyl-CoA. In contrast to degradation pathways of monocyclic aromatic compounds where ring-cleavage is achieved via hydratases, this lyase might represent a new ring-opening strategy for the degradation of polycyclic compounds. Conversion of the potential downstream metabolites pimeloyl-CoA and glutaryl-CoA was proved in cell free extracts, yielding 2,3-dehydropimeloyl-CoA, 3-hydroxypimeloyl-CoA, 3-oxopimeloyl-CoA, glutaconyl-CoA, crotonyl-CoA, 3-hydroxybutyryl-CoA and acetyl-CoA as observable intermediates. This indicates a link to central metabolism via β-oxidation, a non-decarboxylating glutaryl-CoA dehydrogenase and a subsequent glutaconyl-CoA decarboxylase.
Collapse
Affiliation(s)
- Philip Weyrauch
- Biofilm Centre, University of Duisburg-Essen, Essen, Germany.,Institute of Groundwater Ecology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Andrey V Zaytsev
- School of Chemistry, Newcastle University, Newcastle, UK.,Health and Life Sciences, Northumberland University, Newcastle, UK
| | - Susanne Stephan
- Applied Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Lena Kocks
- Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Oliver J Schmitz
- Applied Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | | | | |
Collapse
|
39
|
Anaerobic Biodegradation of Polyaromatic Hydrocarbons by a Sulfate Reducing Bacteria C1Fd Strain. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2017. [DOI: 10.22207/jpam.11.2.18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
40
|
Koelschbach JS, Mouttaki H, Pickl C, Heipieper HJ, Rachel R, Lawson PA, Meckenstock RU. Rectinema cohabitans gen. nov., sp. nov., a rod-shaped spirochaete isolated from an anaerobic naphthalene-degrading enrichment culture. Int J Syst Evol Microbiol 2017; 67:1288-1295. [DOI: 10.1099/ijsem.0.001799] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Janina S Koelschbach
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- Universität Duisburg-Essen, Biofilm Centre, Universitätsstr. 5, 45141 Essen, Germany
| | - Housna Mouttaki
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Carolin Pickl
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Hermann J Heipieper
- Helmholtz Zentrum für Umweltforschung, Department of Environmental Biotechnology, Permoserstr. 15, 04318 Leipzig, Germany
| | - Reinhard Rachel
- Universität Regensburg, Zentrum für Elektronenmikroskopie der Fakultät für Biologie und Vorklinische Medizin, Universitätsstr. 31, 93053 Regensburg, Germany
| | - Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Rainer U Meckenstock
- Universität Duisburg-Essen, Biofilm Centre, Universitätsstr. 5, 45141 Essen, Germany
| |
Collapse
|
41
|
Martirani-Von Abercron SM, Pacheco D, Benito-Santano P, Marín P, Marqués S. Polycyclic Aromatic Hydrocarbon-Induced Changes in Bacterial Community Structure under Anoxic Nitrate Reducing Conditions. Front Microbiol 2016; 7:1775. [PMID: 27877167 PMCID: PMC5099901 DOI: 10.3389/fmicb.2016.01775] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/21/2016] [Indexed: 11/13/2022] Open
Abstract
Although bacterial anaerobic degradation of mono-aromatic compounds has been characterized in depth, the degradation of polycyclic aromatic hydrocarbons (PAHs) such as naphthalene has only started to be understood in sulfate reducing bacteria, and little is known about the anaerobic degradation of PAHs in nitrate reducing bacteria. Starting from a series of environments which had suffered different degrees of hydrocarbon pollution, we used most probable number (MPN) enumeration to detect and quantify the presence of bacterial communities able to degrade several PAHs using nitrate as electron acceptor. We detected the presence of a substantial nitrate reducing community able to degrade naphthalene, 2-methylnaphthalene (2MN), and anthracene in some of the sites. With the aim of isolating strains able to degrade PAHs under denitrifying conditions, we set up a series of enrichment cultures with nitrate as terminal electron acceptor and PAHs as the only carbon source and followed the changes in the bacterial communities throughout the process. Results evidenced changes attributable to the imposed nitrate respiration regime, which in several samples were exacerbated in the presence of the PAHs. The presence of naphthalene or 2MN enriched the community in groups of uncultured and poorly characterized organisms, and notably in the Acidobacteria uncultured group iii1-8, which in some cases was only a minor component of the initial samples. Other phylotypes selected by PAHs in these conditions included Bacilli, which were enriched in naphthalene enrichments. Several nitrate reducing strains showing the capacity to grow on PAHs could be isolated on solid media, although the phenotype could not be reproduced in liquid cultures. Analysis of known PAH anaerobic degradation genes in the original samples and enrichment cultures did not reveal the presence of PAH-related nmsA-like sequences but confirmed the presence of bssA-like genes related to anaerobic toluene degradation. Altogether, our results suggest that PAH degradation by nitrate reducing bacteria may require the contribution of different strains, under culture conditions that still need to be defined.
Collapse
Affiliation(s)
| | - Daniel Pacheco
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Patricia Benito-Santano
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Patricia Marín
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Silvia Marqués
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas Granada, Spain
| |
Collapse
|
42
|
Xie Y, Wang J, Wu Y, Ren C, Song C, Yang J, Yu H, Giesy JP, Zhang X. Using in situ bacterial communities to monitor contaminants in river sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 212:348-357. [PMID: 26866572 DOI: 10.1016/j.envpol.2016.01.031] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 01/12/2016] [Accepted: 01/12/2016] [Indexed: 06/05/2023]
Abstract
Bacterial communities in sediments of human-impacted rivers are exposed to multiple anthropogenic contaminants and eventually lead to biodiversity lost and ecological functions disable. Nanfei River of Anhui province has been contaminated by pollutants from industrial and/or agricultural sources. This study was conducted to investigate the structure of in situ sediment bacterial communities in Nanfei River and to examine the correlation between the different taxonomic components and contaminant concentrations. The bacterial communities were dominated by Proteobacteria, Bacteroidetes and Chloroflexi. Both the profiles of environmental predictors and the composition of microbial communities differed among agriculture, industrial and confluence regions. There were significant associations between bacterial community phylogenies and the measured contaminants in the sediments. Nutrients (TN and TP) and two metals (Cd and Zn) were negatively correlated with the essential "core" of the bacterial interaction network (Betaproteobacteria and Deltaproteobacteria). Metals (Fe, Ni and Zn) and nutrients (TN and TP) had higher impact on bacterial community compositions than PAHs, OPs and PRTs according to the correlation and network analyses. Furthermore, several sensitive candidate genera were identified as potential bioindicators to monitor key contaminants by species contaminant correlation analysis. Overall, in situ bacterial communities could provide a useful tool for monitoring and assessing ecological stressors in freshwater sediments.
Collapse
Affiliation(s)
- Yuwei Xie
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Jizhong Wang
- Laboratory for Nanomineralogy and Environmental Material, School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Yaketon Wu
- Laboratory for Nanomineralogy and Environmental Material, School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Chen Ren
- Laboratory for Nanomineralogy and Environmental Material, School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Chao Song
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - John P Giesy
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China; Department of Veterinary Biomedical Sciences and Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; School of Biological Sciences, University of Hong Kong, Hong Kong Special Administrative Region; Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong Special Administrative Region
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China.
| |
Collapse
|
43
|
Meckenstock RU, Boll M, Mouttaki H, Koelschbach JS, Cunha Tarouco P, Weyrauch P, Dong X, Himmelberg AM. Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons. J Mol Microbiol Biotechnol 2016; 26:92-118. [DOI: 10.1159/000441358] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Aromatic hydrocarbons such as benzene and polycyclic aromatic hydrocarbons (PAHs) are very slowly degraded without molecular oxygen. Here, we review the recent advances in the elucidation of the first known degradation pathways of these environmental hazards. Anaerobic degradation of benzene and PAHs has been successfully documented in the environment by metabolite analysis, compound-specific isotope analysis and microcosm studies. Subsequently, also enrichments and pure cultures were obtained that anaerobically degrade benzene, naphthalene or methylnaphthalene, and even phenanthrene, the largest PAH currently known to be degradable under anoxic conditions. Although such cultures grow very slowly, with doubling times of around 2 weeks, and produce only very little biomass in batch cultures, successful proteogenomic, transcriptomic and biochemical studies revealed novel degradation pathways with exciting biochemical reactions such as for example the carboxylation of naphthalene or the ATP-independent reduction of naphthoyl-coenzyme A. The elucidation of the first anaerobic degradation pathways of naphthalene and methylnaphthalene at the genetic and biochemical level now opens the door to studying the anaerobic metabolism and ecology of anaerobic PAH degraders. This will contribute to assessing the fate of one of the most important contaminant classes in anoxic sediments and aquifers.
Collapse
|
44
|
Vogt C, Lueders T, Richnow HH, Krüger M, von Bergen M, Seifert J. Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders. J Mol Microbiol Biotechnol 2016; 26:195-210. [DOI: 10.1159/000440806] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Stable isotope probing (SIP) techniques have become state-of-the-art in microbial ecology over the last 10 years, allowing for the targeted detection and identification of organisms, metabolic pathways and elemental fluxes active in specific processes within complex microbial communities. For studying anaerobic hydrocarbon-degrading microbial communities, four stable isotope techniques have been used so far: DNA/RNA-SIP, PLFA (phospholipid-derived fatty acids)-SIP, protein-SIP, and single-cell-SIP by nanoSIMS (nanoscale secondary ion mass spectrometry) or confocal Raman microscopy. DNA/RNA-SIP techniques are most frequently applied due to their most meaningful phylogenetic resolution. Especially using <sup>13</sup>C-labeled benzene and toluene as model substrates, many new hydrocarbon degraders have been identified by SIP under various electron acceptor conditions. This has extended the current perspective of the true diversity of anaerobic hydrocarbon degraders relevant in the environment. Syntrophic hydrocarbon degradation was found to be a common mechanism for various electron acceptors. Fundamental concepts and recent advances in SIP are reflected here. A discussion is presented concerning how these techniques generate direct insights into intrinsic hydrocarbon degrader populations in environmental systems and how useful they are for more integrated approaches in the monitoring of contaminated sites and for bioremediation.
Collapse
|
45
|
Heider J, Szaleniec M, Martins BM, Seyhan D, Buckel W, Golding BT. Structure and Function of Benzylsuccinate Synthase and Related Fumarate-Adding Glycyl Radical Enzymes. J Mol Microbiol Biotechnol 2016; 26:29-44. [PMID: 26959246 DOI: 10.1159/000441656] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The pathway of anaerobic toluene degradation is initiated by a remarkable radical-type enantiospecific addition of the chemically inert methyl group to the double bond of a fumarate cosubstrate to yield (R)-benzylsuccinate as the first intermediate, as catalyzed by the glycyl radical enzyme benzylsuccinate synthase. In recent years, it has become clear that benzylsuccinate synthase is the prototype enzyme of a much larger family of fumarate-adding enzymes, which play important roles in the anaerobic metabolism of further aromatic and even aliphatic hydrocarbons. We present an overview on the biochemical properties of benzylsuccinate synthase, as well as its recently solved structure, and present the results of an initial structure-based modeling study on the reaction mechanism. Moreover, we compare the structure of benzylsuccinate synthase with those predicted for different clades of fumarate-adding enzymes, in particular the paralogous enzymes converting p-cresol, 2-methylnaphthalene or n-alkanes.
Collapse
Affiliation(s)
- Johann Heider
- Laboratory of Microbial Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | | | | | | | | | | |
Collapse
|
46
|
Tan B, Jane Fowler S, Laban NA, Dong X, Sensen CW, Foght J, Gieg LM. Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples. THE ISME JOURNAL 2015; 9:2028-45. [PMID: 25734684 PMCID: PMC4542035 DOI: 10.1038/ismej.2015.22] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 01/07/2015] [Accepted: 01/09/2015] [Indexed: 11/09/2022]
Abstract
Methanogenic hydrocarbon metabolism is a key process in subsurface oil reservoirs and hydrocarbon-contaminated environments and thus warrants greater understanding to improve current technologies for fossil fuel extraction and bioremediation. In this study, three hydrocarbon-degrading methanogenic cultures established from two geographically distinct environments and incubated with different hydrocarbon substrates (added as single hydrocarbons or as mixtures) were subjected to metagenomic and 16S rRNA gene pyrosequencing to test whether these differences affect the genetic potential and composition of the communities. Enrichment of different putative hydrocarbon-degrading bacteria in each culture appeared to be substrate dependent, though all cultures contained both acetate- and H2-utilizing methanogens. Despite differing hydrocarbon substrates and inoculum sources, all three cultures harbored genes for hydrocarbon activation by fumarate addition (bssA, assA, nmsA) and carboxylation (abcA, ancA), along with those for associated downstream pathways (bbs, bcr, bam), though the cultures incubated with hydrocarbon mixtures contained a broader diversity of fumarate addition genes. A comparative metagenomic analysis of the three cultures showed that they were functionally redundant despite their enrichment backgrounds, sharing multiple features associated with syntrophic hydrocarbon conversion to methane. In addition, a comparative analysis of the culture metagenomes with those of 41 environmental samples (containing varying proportions of methanogens) showed that the three cultures were functionally most similar to each other but distinct from other environments, including hydrocarbon-impacted environments (for example, oil sands tailings ponds and oil-affected marine sediments). This study provides a basis for understanding key functions and environmental selection in methanogenic hydrocarbon-associated communities.
Collapse
Affiliation(s)
- Boonfei Tan
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - S Jane Fowler
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Nidal Abu Laban
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Xiaoli Dong
- Visual Genomics Centre, Faculty of Medicine, Calgary, Alberta, Canada
| | | | - Julia Foght
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Lisa M Gieg
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
47
|
Funk MA, Marsh ENG, Drennan CL. Substrate-bound structures of benzylsuccinate synthase reveal how toluene is activated in anaerobic hydrocarbon degradation. J Biol Chem 2015. [PMID: 26224635 DOI: 10.1074/jbc.m115.670737] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Various bacteria perform anaerobic degradation of small hydrocarbons as a source of energy and cellular carbon. To activate non-reactive hydrocarbons such as toluene, enzymes conjugate these molecules to fumarate in a radical-catalyzed, C-C bond-forming reaction. We have determined x-ray crystal structures of the glycyl radical enzyme that catalyzes the addition of toluene to fumarate, benzylsuccinate synthase (BSS), in two oligomeric states with fumarate alone or with both substrates. We find that fumarate is secured at the bottom of a long active site cavity with toluene bound directly above it. The two substrates adopt orientations that appear ideal for radical-mediated C-C bond formation; the methyl group of toluene is positioned between fumarate and a cysteine that forms a thiyl radical during catalysis, which is in turn adjacent to the glycine that serves as a radical storage residue. Toluene is held in place by fumarate on one face and tight packing by hydrophobic residues on the other face and sides. These hydrophobic residues appear to become ordered, thus encapsulating toluene, only in the presence of BSSβ, a small protein subunit that forms a tight complex with BSSα, the catalytic subunit. Enzymes related to BSS are able to metabolize a wide range of hydrocarbons through attachment to fumarate. Using our structures as a guide, we have constructed homology models of several of these "X-succinate synthases" and determined conservation patterns that will be useful in understanding the basis for catalysis and specificity in this family of enzymes.
Collapse
Affiliation(s)
| | - E Neil G Marsh
- the Department of Chemistry and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Catherine L Drennan
- From the Departments of Chemistry and Biology and the Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 and
| |
Collapse
|
48
|
A Comprehensive Review of Aliphatic Hydrocarbon Biodegradation by Bacteria. Appl Biochem Biotechnol 2015; 176:670-99. [PMID: 25935219 DOI: 10.1007/s12010-015-1603-5] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 03/31/2015] [Indexed: 02/07/2023]
Abstract
Hydrocarbons are relatively recalcitrant compounds and are classified as high-priority pollutants. However, these compounds are slowly degraded by a large variety of microorganisms. Bacteria are able to degrade aliphatic saturated and unsaturated hydrocarbons via both aerobic and anaerobic pathways. Branched hydrocarbons and cyclic hydrocarbons are also degraded by bacteria. The aerobic bacteria use different types of oxygenases, including monooxygenase, cytochrome-dependent oxygenase and dioxygenase, to insert one or two atoms of oxygen into their targets. Anaerobic bacteria, on the other hand, employ a variety of simple organic and inorganic molecules, including sulphate, nitrate, carbonate and metals, for hydrocarbon oxidation.
Collapse
|
49
|
Jaekel U, Zedelius J, Wilkes H, Musat F. Anaerobic degradation of cyclohexane by sulfate-reducing bacteria from hydrocarbon-contaminated marine sediments. Front Microbiol 2015; 6:116. [PMID: 25806023 PMCID: PMC4352924 DOI: 10.3389/fmicb.2015.00116] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 01/29/2015] [Indexed: 11/13/2022] Open
Abstract
The fate of cyclohexane, often used as a model compound for the biodegradation of cyclic alkanes due to its abundance in crude oils, in anoxic marine sediments has been poorly investigated. In the present study, we obtained an enrichment culture of cyclohexane-degrading sulfate-reducing bacteria from hydrocarbon-contaminated intertidal marine sediments. Microscopic analyses showed an apparent dominance by oval cells of 1.5 × 0.8 μm. Analysis of a 16S rRNA gene library, followed by whole-cell hybridization with group- and sequence-specific oligonucleotide probes showed that these cells belonged to a single phylotype, and were accounting for more than 80% of the total cell number. The dominant phylotype, affiliated with the Desulfosarcina-Desulfococcus cluster of the Deltaproteobacteria, is proposed to be responsible for the degradation of cyclohexane. Quantitative growth experiments showed that cyclohexane degradation was coupled with the stoichiometric reduction of sulfate to sulfide. Substrate response tests corroborated with hybridization with a sequence-specific oligonucleotide probe suggested that the dominant phylotype apparently was able to degrade other cyclic and n-alkanes, including the gaseous alkane n-butane. Based on GC-MS analyses of culture extracts cyclohexylsuccinate was identified as a metabolite, indicating an activation of cyclohexane by addition to fumarate. Other metabolites detected were 3-cyclohexylpropionate and cyclohexanecarboxylate providing evidence that the overall degradation pathway of cyclohexane under anoxic conditions is analogous to that of n-alkanes.
Collapse
Affiliation(s)
- Ulrike Jaekel
- Department of Microbiology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Johannes Zedelius
- Department of Microbiology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Heinz Wilkes
- Organic Geochemistry, Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences Potsdam, Germany
| | - Florin Musat
- Department of Microbiology, Max Planck Institute for Marine Microbiology Bremen, Germany ; Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany
| |
Collapse
|
50
|
Kümmel S, Herbst FA, Bahr A, Duarte M, Pieper DH, Jehmlich N, Seifert J, von Bergen M, Bombach P, Richnow HH, Vogt C. Anaerobic naphthalene degradation by sulfate-reducing Desulfobacteraceae from various anoxic aquifers. FEMS Microbiol Ecol 2015; 91:fiv006. [PMID: 25764566 DOI: 10.1093/femsec/fiv006] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAH) are widespread and persistent environmental contaminants, especially in oxygen-free environments. The occurrence of anaerobic PAH-degrading bacteria and their underlying metabolic pathways are rarely known. In this study, PAH degraders were enriched in laboratory microcosms under sulfate-reducing conditions using groundwater and sediment samples from four PAH-contaminated aquifers. Five enrichment cultures were obtained showing sulfate-dependent naphthalene degradation. Mineralization of naphthalene was demonstrated by the formation of sulfide concomitant with the depletion of naphthalene and the development of (13)C-labeled CO2 from [(13)C6]-naphthalene. 16S rRNA gene and metaproteome analyses revealed that organisms related to Desulfobacterium str. N47 were the main naphthalene degraders in four enrichment cultures. Protein sequences highly similar to enzymes of the naphthalene degradation pathway of N47 were identified, suggesting that naphthalene was activated by a carboxylase, and that the central metabolite 2-naphthoyl-CoA was further reduced by two reductases. The data indicate an importance of members of the family Desulfobacteraceae for naphthalene degradation under sulfate-reducing conditions in freshwater environments.
Collapse
Affiliation(s)
- Steffen Kümmel
- UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstraße 15, D-04318 Leipzig, Germany University of Freiburg, Faculty of Biology, Schaenzlestraße 1, D-79104 Freiburg, Germany
| | - Florian-Alexander Herbst
- UFZ - Helmholtz Centre for Environmental Research, Department of Proteomics, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Arne Bahr
- UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Márcia Duarte
- Helmholtz Centre for Infection Research - HZI, Microbial Interactions and Processes Research Group, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Dietmar H Pieper
- Helmholtz Centre for Infection Research - HZI, Microbial Interactions and Processes Research Group, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Nico Jehmlich
- UFZ - Helmholtz Centre for Environmental Research, Department of Proteomics, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Jana Seifert
- University of Freiburg, Faculty of Biology, Schaenzlestraße 1, D-79104 Freiburg, Germany University of Hohenheim, Faculty of Agricultural Sciences, Emil-Wolff-Straße 8-10, D-70599 Stuttgart, Germany
| | - Martin von Bergen
- University of Freiburg, Faculty of Biology, Schaenzlestraße 1, D-79104 Freiburg, Germany UFZ - Helmholtz Centre for Environmental Research, Department of Metabolomics, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Petra Bombach
- UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Hans H Richnow
- UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Carsten Vogt
- UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstraße 15, D-04318 Leipzig, Germany
| |
Collapse
|